In my opinion, OoT and LttP trump all. Really have not enjoyed a Zelda game since except for a bit of Minish Cap.
While I had TP, it just felt like I was going through the motions to beat the game. I had no drive to find any extras at all. I do not have a Wii anymore, but i'd imagine the same could be said of SS. Maybe Wind Waker took too much out of me because while it was a good game, I did not enjoy the sailing. Watched a friend play SS for a while and it looks like the Flying is similar to the sailing. He says that there is not really an overworld. You revisit alot of places and so on. Granted, I have not played it myself but he took about 50 hours to beat it, so he may know what he is talking about.
That said, I just have not enjoyed Zelda games as games. Ocarina of Time and Link to the Past had me exploring the overworld, trying to find all the hidden items and heart pieces. I felt as though I could really do what I wanted. I did not feel hampered by story progression. When I beat TP I really felt pushed to finish the story, I never enjoyed looking for anything. After the first 2 dungeons I had a mindset of "I paid $49 for this, just finish it".
Maybe I am too much of a nostalgic person but the new Zelda games of late have not really grabbed me like the past generation of them did.
That being said, when i get my tax returns, I plan of purchasing a 3DS and OoT3d. I am holding out that Nintendo will make a couple good Zelda games for the 3DS.
Oh and I 100% prefer realistic to cartoon when it comes to the 3d Zelda games. For the 2d, I enjoy all the styles.
The only 3d cartoon styled games I really think had great graphics when the Kingdom Hearts games, but those were not cel-shaded best as I can remember. Just anime styled.